Revert file permission changes in local git repository.. Very useful when you change permissions due to working on a samba share. Lifted from: http://stackoverflow.com/questions/2517339/git-how-to-recover-the-file-permissions-git-thinks-the-file-should-be

gistfile1.sh

git diff -p \
    | grep -E '^(diff|old mode|new mode)' \
    | sed -e 's/^old/NEW/;s/^new/old/;s/^NEW/new/' \
    | git apply

If this solution does not work for you, I have found two possible causes -

1. Your git clone is on an ExFAT formatted volume. There is no fix for this, and no commands will help. ExFAT doesn't support file permissions. You can only configure git to ignore file permissions, or reformat the drive using something more suitable.
2. Your git clone is on a volume shared via Apple File Sharing and has an ACL at the root of the volume. If that's you, good luck, and I have no idea, but maybe this tip will send you in the right direction!

It isn't a solution, in that it doesn't change or fix file permissions, but if you are stuck with one of the above, it may ease the pain to set:

git config core.fileMode false

though using this setting is highly not recommended generally.

@martynov-dm you should run git permission-resetb not git apply